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Viewing changes to src/org/openscience/cdk/modeling/forcefield/ForceField.java

  • Committer: Bazaar Package Importer
  • Author(s): Paul Cager
  • Date: 2008-04-09 21:17:53 UTC
  • Revision ID: james.westby@ubuntu.com-20080409211753-46lmjw5z8mx5pd8d
Tags: upstream-1.0.2
Import upstream version 1.0.2

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src/org/openscience/cdk/modeling/forcefield/ForceField.java
 
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package org.openscience.cdk.modeling.forcefield;
 
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import javax.vecmath.GVector;
 
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import org.openscience.cdk.AtomContainer;
 
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import org.openscience.cdk.Molecule;
 
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import org.openscience.cdk.graph.ConnectivityChecker;
 
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//import org.openscience.cdk.tools.LoggingTool;
 
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/**
 
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 *  To work with the coordinates of the molecule, like get the 3d coordinates of the atoms or 
 
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 *  calculate the distance between two atoms.
 
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 *@author     vlabarta
 
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 *@cdk.module     forcefield
 
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 *
 
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 */
 
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public class ForceField extends GeometricMinimizer{
 
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        private String potentialFunction="mmff94";
 
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        boolean sdm_flag=true;
 
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        boolean cgm_flag=true;
 
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        boolean nrm_flag=true;
 
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        //private LoggingTool logger;
 
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        /**
 
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         *  Constructor for the ForceField object
 
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         */
 
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        public ForceField() {        
 
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                //logger = new LoggingTool(this);
 
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        }
 
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        public ForceField(Molecule molecule) throws Exception {
 
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                setMolecule(molecule, false);
 
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                //logger = new LoggingTool(this);
 
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        }
 
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        public void setPotentialFunction(String potentialName){
 
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                potentialFunction=potentialName;
 
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        }
 
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        public void setUsedGMMethods(boolean sdm, boolean cgm,boolean nrm){
 
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               sdm_flag=sdm;
 
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               cgm_flag=cgm;
 
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               nrm_flag=nrm;
 
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        }
 
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        public void minimize( ) throws Exception{
 
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                long start, stop;
 
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                if (!ConnectivityChecker.isConnected(molecule)) {
 
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                        throw new Exception("CDKError: Molecule is NOT connected,could not layout.");
 
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                }
 
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                GVector moleculeCoords = new GVector(3);
 
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                MMFF94EnergyFunction mmff94PF=null;
 
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                if (potentialFunction=="mmff94"){
 
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                    //logger.debug("SET POTENTIAL FUNCTION TO MMFF94");
 
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                    setMMFF94Tables(molecule);
 
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                    mmff94PF=new MMFF94EnergyFunction((AtomContainer)molecule,getPotentialParameterSet());
 
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                        //logger.debug("PotentialFunction set:"+potentialFunction+", Hashtable:" +getPotentialParameterSet().size());
 
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                }
 
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                moleculeCoords.setSize(molecule.getAtomCount() * 3);
 
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                moleculeCoords.set(ForceFieldTools.getCoordinates3xNVector((AtomContainer)molecule));
 
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                //logger.debug("PotentialFunction set:"+potentialFunction+" Molecule Coords set:"+moleculeCoords.getSize()+" Hashtable:"+getPotentialParameterSet().size());
 
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                //logger.debug(moleculeCoords.toString());
 
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                start = System.currentTimeMillis();
 
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                //logger.debug("Starting minmization at " + start);
 
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                if (sdm_flag) steepestDescentsMinimization(moleculeCoords,mmff94PF);
 
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                if (cgm_flag)conjugateGradientMinimization(moleculeCoords, mmff94PF);
 
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                //conjugateGradientMinimization(moleculeCoords, tpf);
 
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                stop = System.currentTimeMillis();
 
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                //logger.debug("Finished minmization at " + stop);
 
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                //if ((stop - start)/1000 < 60) {
 
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                        //logger.debug("Time for minimization: " + (stop - start)/1000 + " sec");
 
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                //}
 
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                //      logger.debug("Time for minimization: " + (stop - start)/60000 + " min");
 
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                //}
 
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                //logger.debug("Minimization READY");
 
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                //ForceFieldTools.assignCoordinatesToMolecule(moleculeCoords, (AtomContainer) molecule); 
 
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        }
 
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}
 
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